CRAN requires the check problems on this package to be fixed before 2026-08-15 or it will be archived.

vcfppR

0.8.4

Rapid Manipulation of the Variant Call Format (VCF)

1packages depend

4.5Kdownloads / year

77.7%test coverage

13/13checks pass

Overview

About

Maintained by Zilong LiFirst published 2023-12-1416 releasesCRAN page ↗GitHub ↗

The 'vcfpp.h' (https://github.com/Zilong-Li/vcfpp) provides an easy-to-use 'C++' 'API' of 'htslib', offering full functionality for manipulating Variant Call Format (VCF) files. The 'vcfppR' package serves as the R bindings of the 'vcfpp.h' library, enabling rapid processing of both compressed and uncompressed VCF files. Explore a range of powerful features for efficient VCF data manipulation.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("vcfppR", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("Zilong-Li/vcfppR")

Development version from Zilong-Li/vcfppR. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-vcfppr

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

Health

CRAN checks

13OK

Slowest check: 6.1 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 1.11

77.7%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-08-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-07-16
12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 1 earlier snapshots

NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 302 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 89%
Documented parameters: 100%
Return-value docs: 80%
References docs: 0%

Downloads

4.5K

CRAN downloads in the past year

Rank #10,453 · ~12/day · ~373/mo

Releases R versions

Daily download trend is not available in this view yet.

26630 days

96190 days

4.5K1 year

Compare downloads with other packages →

Also on494 r2u

Repository

GitHub ↗ zilong-li/vcfppr

20Stars

4Forks

0Open issues

0Open PRs

13Releases

255Commits

3Contributors

bioinformaticsfastrvcfhtslibpopulation-geneticspopulation-genomicsrstatsvcf-data

255 commits · Last activity 2026-03-31 · 0% stars, 30d

Stars over time

2025-04-09 · 152026-07-07 · 20

Repository practices

Upstream repositoryBeta

6 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/zilong-li/vcfppr on 2026-08-03.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

Makefile

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Show all practices

Coverage (1)

.covrignore

Governance and community (1)

PR template

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.6.0

Imports (4)

Rcppmethodsstatsutils

LinkingTo (1)

Rcpp

Suggests (4)

knitrcodetoolsrmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

BinaryDosage

Code & Tests

People & History

People (2)

Maintainer (1)

Zilong Li

Author, Maintainer

Authors (1)

Zilong Li

Author, Maintainer

Bonfield, James K and Marshall, John and Danecek, Petr and Li, Heng and Ohan, Valeriu and Whitwham, Andrew and Keane, Thomas and Davies, Robert M

Listed in earlier versions (1)

Bonfield, James K and Marshall, John and Danecek, Petr and Li, Heng

no longer listed · 0.3.5 to 0.4.0

Package Timeline

16 releases. Pick two to compare their code metrics. R releases are shown for context.

0.8.4Latest
2026-08-04 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
0.8.3
2026-04-01 · diff ↗
0.8.2
2025-11-06 · diff ↗
0.8.1
2025-08-25 · diff ↗
0.8.0
2025-07-02 · diff ↗
R
R 4.5.0 released · 2025-04-11
0.7.6
2025-03-31 · diff ↗
0.7.1
2024-12-26 · diff ↗
0.7.0
2024-12-21 · diff ↗
0.6.0
2024-09-30 · diff ↗
0.5.0
2024-09-22 · diff ↗
0.4.6
2024-05-24 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.4.5
2024-04-08 · diff ↗
0.4.3
2024-03-27 · diff ↗

Show 6 earlier events

unarchivedReturned to CRAN
2024-03-27
archivedRemoved from CRAN
2024-03-15
issues were not corrected in time
0.4.0
2024-02-26 · diff ↗
0.3.8
2024-01-14 · diff ↗
0.3.5
2023-12-14
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-12-14
Total releases: 16 / 3 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.6.0
Download size: 2.7 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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